I suspect that we might be falling foul of some code in export.c intended to drop deletes:

/*
* Skip BitKeeper/ files (but pass deletes..)
*
* Email Note from Wayne Scott:
* In general the only changes to files in the deleted
* directory are when they are moved to that directory.
* This code requires that its starting location or the ending
* location must be outside of bitkeeper. We don't need
* patches with changes for files that are deleted. We just
* need the patch to have the delete.
*/

I suspect it shouldn't be skipping BitKeeper files if the undocumented -a is passed: